3814d8eec23ed1c9f539f669383099eb605dbbcd
mspeir
Sat Sep 26 18:18:00 2026 -0700
Regulation FAQ: link hgCustom as well as the custom track help, refs #24610
diff --git src/hg/htdocs/FAQ/FAQregulation.html src/hg/htdocs/FAQ/FAQregulation.html
index debed8a8caa..8e06956e0c6 100755
--- src/hg/htdocs/FAQ/FAQregulation.html
+++ src/hg/htdocs/FAQ/FAQregulation.html
@@ -120,33 +120,34 @@
experiments that were available when it was built, so if your factor is absent from ReMap there
may be no public ChIP-seq for it in that organism. The
ReMap website lets you search by target
and download the peaks per factor, and that is the quickest way to check.
If the experiment exists but is newer than our tracks, or was done in a cell type we do not
carry, you will need to load the data yourself as a custom track. The usual sources are:
-
The ENCODE portal, for anything
produced by ENCODE. This is the easiest case, because the portal will send the data
straight to our browser for you. See the next question.
-
GEO, for data submitted
alongside a publication. Many GEO submissions include processed peak files as supplementary
- material, usually BED or narrowPeak, which you can load as a
- custom track after checking that the
- coordinates match the assembly you are using.
+ material, usually BED or narrowPeak, which you can
+ load as a custom track at
+ Add Custom Tracks, after checking that the coordinates
+ match the assembly you are using.
-
SRA, for raw sequencing reads.
The Browser cannot display SRA data. Raw reads have to be aligned and peak-called before there
is anything to show, which is a job for a sequence analysis pipeline rather than for us.
How do I display ENCODE data that is not already a track?
You do not need to download anything or write a custom track by hand. The ENCODE portal will
open its data in the Genome Browser for you.
-
Search the ENCODE portal for what you want, narrowing the results with the filters